SfePy

sfepy@python.org

3 participants
815 discussions

Execution Time Problem on 3D uniaxial compressive simulation #649 from Github

by Yang, Kedi

Hi guys, Currently, I am using Sfepy to simulate a 3D geometry model with a uniaxial displacement to find out the von Mises strength and the total execution time for the simulation is about *40 mins with 8G RAM*. Besides, 94% of the RAM is occupied when the program is running. I am not sure what is causing this execution time to take that long and what I could do to shorten the execution time. The geometry model was inputted from an Abaqus input-file with 5514 vertices and 4417 cells. Also, I have checked the execution time line-by-line and found that the most time consumable step is defined as: state = pb.solve(status=status) In this case, I am supposing the solving process used most of the RAM and causing the timing issue. The mesh file and our code is attached. Thank you and best regards! Kedi Yang

6 days, 6 hours

error of gen_yeoh_tl_up_interactive.py

by Takuo Fujita

Hi, Thank you for the release of 2020.3. I appreciate it. I tried the new example, gen_yeoh_tl_up_interactive.py. I encountered the error below. $python examples/large_deformation/gen_yeoh_tl_up_interactive.py Traceback (most recent call last): File "examples/large_deformation/gen_yeoh_tl_up_interactive.py", line 424, in <module> main(args) File "examples/large_deformation/gen_yeoh_tl_up_interactive.py", line 327, in main integral, omega, m1=m_1, v=v, u=u) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/terms/terms.py", line 342, in new raise ValueError(msg) ValueError: term 'dw_tl_he_genyeoh' is not in ['d_of_ns_min_grad', 'd_of_ns_surf_min_d_press', 'd_sd_convect', 'd_sd_diffusion', 'd_sd_div', 'd_sd_div_grad', 'd_sd_lin_elastic', 'd_sd_st_grad_div', 'd_sd_st_pspg_c', 'd_sd_st_pspg_p', 'd_sd_st_supg_c', 'd_sd_surface_integrate', 'd_sd_volume_dot', 'd_sum_vals', 'd_surface', 'd_surface_flux', 'd_surface_moment', 'd_tl_surface_flux', 'd_tl_volume_surface', 'd_volume', 'd_volume_surface', 'dw_adj_convect1', 'dw_adj_convect2', 'dw_adj_div_grad', 'dw_advect_div_free', 'dw_bc_newton', 'dw_biot', 'dw_biot_eth', 'dw_biot_th', 'dw_contact', 'dw_contact_plane', 'dw_contact_sphere', 'dw_convect', 'dw_convect_v_grad_s', 'dw_diffusion', 'dw_diffusion_coupling', 'dw_diffusion_r', 'dw_div', 'dw_div_grad', 'dw_elastic_wave', 'dw_elastic_wave_cauchy', 'dw_electric_source', 'dw_jump', 'dw_laplace', 'dw_lin_convect', 'dw_lin_convect2', 'dw_lin_elastic', 'dw_lin_elastic_eth', 'dw_lin_elastic_iso', 'dw_lin_elastic_th', 'dw_lin_prestress', 'dw_lin_strain_fib', 'dw_non_penetration', 'dw_non_penetration_p', 'dw_nonsym_elastic', 'dw_of_ns_surf_min_d_press_diff', 'dw_piezo_coupling', 'dw_point_load', 'dw_point_lspring', 'dw_s_dot_grad_i_s', 'dw_s_dot_mgrad_s', 'dw_shell10x', 'dw_st_adj1_supg_p', 'dw_st_adj2_supg_p', 'dw_st_adj_supg_c', 'dw_st_grad_div', 'dw_st_pspg_c', 'dw_st_pspg_p', 'dw_st_supg_c', 'dw_st_supg_p', 'dw_stokes', 'dw_stokes_wave', 'dw_stokes_wave_div', 'dw_surface_dot', 'dw_surface_flux', 'dw_surface_integrate', 'dw_surface_ltr', 'dw_surface_ndot', 'dw_tl_bulk_active', 'dw_tl_bulk_penalty', 'dw_tl_bulk_pressure', 'dw_tl_diffusion', 'dw_tl_fib_a', 'dw_tl_he_mooney_rivlin', 'dw_tl_he_neohook', 'dw_tl_membrane', 'dw_tl_surface_traction', 'dw_tl_volume', 'dw_ul_bulk_penalty', 'dw_ul_bulk_pressure', 'dw_ul_compressible', 'dw_ul_he_mooney_rivlin', 'dw_ul_he_neohook', 'dw_ul_volume', 'dw_v_dot_grad_s', 'dw_vm_dot_s', 'dw_volume_dot', 'dw_volume_dot_w_scalar_eth', 'dw_volume_dot_w_scalar_th', 'dw_volume_integrate', 'dw_volume_lvf', 'dw_zero', 'ev_biot_stress', 'ev_cauchy_strain', 'ev_cauchy_strain_s', 'ev_cauchy_stress', 'ev_cauchy_stress_eth', 'ev_cauchy_stress_th', 'ev_def_grad', 'ev_diffusion_velocity', 'ev_div', 'ev_grad', 'ev_piezo_strain', 'ev_piezo_stress', 'ev_surface_div', 'ev_surface_grad', 'ev_surface_integrate', 'ev_surface_integrate_mat', 'ev_volume_integrate', 'ev_volume_integrate_mat'] $ What should I do to solve the error? Should I edit terms.py? Best regards, Takuo

2 weeks, 1 day

ANN: SfePy 2020.3

by Robert Cimrman

I am pleased to announce the release of SfePy 2020.3. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by finite element methods. It is distributed under the new BSD license. Home page: https://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - new script for visualizations based on pyvista - generalized Yeoh hyperelastic term + example For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Jan Heczko Vladimir Lukes

3 weeks, 1 day

[sfepy]

by Takuo Fujita

Hi sfepy expert, I tried 1 hexa analysis with the attached file, but encountered the error below. The error seems due to unmatched load shape. Coud you give me an instruction? Best regards, Takuo $python linear_elastic_1hexa.py f Material:f constant_names: set() datas: dict with keys: [] extra_args: dict with keys: [] flags: dict with keys: [] function: ConstantFunction:get_constants_val is_constant: True kind: time-dependent mode: None name: f special_names: set() sfepy: saving regions as groups... sfepy: Omega sfepy: origin sfepy: xyz010 sfepy: xyz001 sfepy: xyz011 sfepy: xyz100 sfepy: x1 sfepy: ...done sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (71, 71) sfepy: assembling matrix graph... sfepy: ...done in 0.00 s sfepy: matrix structural nonzeros: 5041 (1.00e+00% fill) sfepy: updating variables... sfepy: ...done sfepy: updating materials... sfepy: m sfepy: f sfepy: ...done in 0.00 s sfepy: allowed argument shapes for term "-1.0 * dw_point_load.0.x1(f.val, v)": sfepy: [{'material': '.: N', 'virtual': ('N', None)}] sfepy: actual argument shapes: sfepy: {"material:('f', 'val')": (0, 0, 0, 0), 'virtual:v': (3,)} sfepy: giving up! Traceback (most recent call last): File "linear_elastic_1hexa.py", line 93, in <module> state = pb.solve(status=status) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/discrete/problem.py", line 1414, in solve status=status) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/solvers/ts_solvers.py", line 34, in _standard_ts_call status=status, **kwargs) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/solvers/ts_solvers.py", line 73, in __call__ vec = nls(vec0) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/solvers/nls.py", line 257, in __call__ vec_r = fun(vec_x) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/discrete/evaluate.py", line 73, in eval_residual vec_r = self.problem.equations.eval_residuals(vec) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/discrete/equations.py", line 701, in eval_residuals self.evaluate(mode='weak', dw_mode='vector', asm_obj=out) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/discrete/equations.py", line 634, in evaluate term_mode=term_mode, asm_obj=asm_obj) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/discrete/equations.py", line 853, in evaluate ret_status=True) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/terms/terms.py", line 1436, in evaluate self.check_shapes(*args) File "/home/pyontaku14/anaconda3/lib/python3.7/site-packages/sfepy/terms/terms.py", line 1274, in check_shapes % term_str) ValueError: wrong arguments shapes for "-1.0 * dw_point_load.0.x1(f.val, v)" term! (see above) $

1 month, 2 weeks

Error in 5 hexas linear static analysis

by Takuo Fujita

Hi sfepy expert, I tried 5 hexas linear static analysis and encountered the following error. Could you please tell me what should be corrected? Best regards, Takuo sfepy: allowed argument shapes for term "+1.0 * dw_lin_elastic_iso.2.Omega(solid.D, v, u)": sfepy: [{'material_1': '1, 1', 'material_2': '1, 1', 'virtual': ('D', 'state'), 'state': 'D', 'parameter_1': 'D', 'parameter_2': 'D'}] sfepy: actual argument shapes: sfepy: {"material_2:('solid', 'D')": (6, 6), 'virtual:v': (3,), 'state:u': (3,)} sfepy: giving up! Traceback (most recent call last): File "/home/pyontaku14/sfepy/simple.py", line 182, in <module> main() File "/home/pyontaku14/sfepy/simple.py", line 179, in main app() File "/home/pyontaku14/sfepy/sfepy/applications/application.py", line 29, in call_basic return self.call(**kwargs) File "/home/pyontaku14/sfepy/sfepy/applications/pde_solver_app.py", line 228, in call post_process_hook_final=self.post_process_hook_final) File "/home/pyontaku14/sfepy/sfepy/discrete/problem.py", line 1435, in solve status=status) File "/home/pyontaku14/sfepy/sfepy/solvers/ts_solvers.py", line 34, in _standard_ts_call status=status, **kwargs) File "/home/pyontaku14/sfepy/sfepy/solvers/ts_solvers.py", line 73, in __call__ vec = nls(vec0) File "/home/pyontaku14/sfepy/sfepy/solvers/nls.py", line 257, in __call__ vec_r = fun(vec_x) File "/home/pyontaku14/sfepy/sfepy/discrete/evaluate.py", line 73, in eval_residual vec_r = self.problem.equations.eval_residuals(vec) File "/home/pyontaku14/sfepy/sfepy/discrete/equations.py", line 702, in eval_residuals self.evaluate(mode='weak', dw_mode='vector', asm_obj=out) File "/home/pyontaku14/sfepy/sfepy/discrete/equations.py", line 635, in evaluate term_mode=term_mode, asm_obj=asm_obj) File "/home/pyontaku14/sfepy/sfepy/discrete/equations.py", line 854, in evaluate ret_status=True) File "/home/pyontaku14/sfepy/sfepy/terms/terms.py", line 1436, in evaluate self.check_shapes(*args) File "/home/pyontaku14/sfepy/sfepy/terms/terms.py", line 1274, in check_shapes % term_str) ValueError: wrong arguments shapes for "+1.0 * dw_lin_elastic_iso.2.Omega(solid.D, v, u)" term! (see above)

1 month, 4 weeks

Query on sfepy for Finite element analysis

by Aanchal Jasuja

Hello, We are trying to use sfepy for FEM analysis. However, we have a couple of queries about sfepy. 1. We couldn't find any examples for 1-D line element modelling, although it says so in the description. Can sfepy be used for it or just for plates & shells? 2. According to the manual, the outputs are in the form of stresses & strains. Is there any possible way to directly get results in the form of bending moment, shear force, reactions etc. ? We would really appreciate your support response at the earliest convenience. Thank you Regards Aanchal Jasuja

2 months, 2 weeks

trying to create animation (following documentation)

by francoisbrest＠hotmail.fr

Hello, I am trying to reproduce an example from the documentation to create an animation. (Windows10, Anaconda python 3.6.10 h9f7ef89_2, sfepy 2020.2 py36h7725771_0 conda-forge) Inside a Jupyter-notebook, I have done: !copy c:\ProgramData\Anaconda3\lib\site-packages\sfepy\examples\diffusion\time_poisson.py . !c:\ProgramData\Anaconda3\python.exe c:\ProgramData\Anaconda3\lib\site-packages\sfepy\script\simple.py time_poisson.py -s #everything OK #I can view each individual vtk #But I cannot create the animation !c:\ProgramData\Anaconda3\python.exe c:\ProgramData\Anaconda3\lib\site-packages\sfepy\script\postproc.py c:\ProgramData\Anaconda3\Scripts\NOTEBOOKS\cylinder.??.vtk -a mov Traceback (most recent call last): File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\script\postproc.py", line 513, in <module> main() File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\script\postproc.py", line 503, in main view = view_file(filenames, filter_names, options) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\script\postproc.py", line 281, in view_file domain_specific=options.domain_specific) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\postprocess\viewer.py", line 919, in call_mlab offscreen=self.offscreen) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\postprocess\sources.py", line 68, in create_file_source return GenericFileSource(filename, **kwargs) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\postprocess\sources.py", line 212, in __init__ self.read_common(self.filename) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\postprocess\sources.py", line 218, in read_common self.mesh = Mesh.from_file(filename) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\discrete\fem\mesh.py", line 220, in from_file mesh = io.read(mesh, omit_facets=omit_facets) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\discrete\fem\meshio.py", line 535, in read fd = open(self.filename, 'r') OSError: [Errno 22] Invalid argument: 'c:\\ProgramData\\Anaconda3\\Scripts\\NOTEBOOKS\\cylinder.??.vtk' #Same problem with (remplacing ?? by *) !c:\ProgramData\Anaconda3\python.exe c:\ProgramData\Anaconda3\lib\site-packages\sfepy\script\postproc.py c:\ProgramData\Anaconda3\Scripts\NOTEBOOKS\cylinder.*.vtk -a mov #N.B. Python has no problem to find ffmpeg !ffmpeg -help #is OK #same problem when I run the command from the terminal (cmd window) c:\ProgramData\Anaconda3\python.exe c:\ProgramData\Anaconda3\lib\site-packages\sfepy\script\postproc.py c:\ProgramData\Anaconda3\Scripts\NOTEBOOKS\cylinder.*.vtk -a mov *meshio.py, line 535, fd = open(self.filename, 'r') does not want to open self.filename; there is a problem with the generic filename extraction ?* Any help appreciated. F.K. P.S. Of course, when I run python postproc.py -a mov on a specific file (say cylinder.00.vtk), I get an error: File "postproc.py", line 508, in main view.save_animation(options.filename) File "c:\ProgramData\Anaconda3\lib\site-packages\sfepy\postprocess\viewer.py", line 345, in save_animation self.set_step.step = step AttributeError: 'Viewer' object has no attribute 'set_step'

3 months, 2 weeks

ANN: SfePy 2020.2

by Robert Cimrman

I am pleased to announce the release of SfePy 2020.2. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by finite element methods. It is distributed under the new BSD license. Home page: https://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - discontinuous Galerkin method implementation and examples - new website look - memory usage improvements For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Jan Heczko Lubos Kejzlar Vladimir Lukes Tomáš Zítka

3 months, 3 weeks

pickle.dump

by francoisbrest＠hotmail.fr

Hello, I am new to SfePy (it looks amazing) I have a question: Is it possible to dump a state variable ? from sfepy.discrete import Problem problem = Problem.from_conf_file( "C:/ProgramData/Anaconda3/Lib/site-packages/sfepy/examples/linear_elasticity/its2D_1.py") state = problem.solve() from pickle import dump with open("state.dat","wb") as f: dump(state,f) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-18-15429a83d7eb> in <module> 1 from pickle import dump 2 with open("state.dat","wb") as f: ----> 3 dump(state,f) C:\ProgramData\Anaconda3\lib\site-packages\sfepy\discrete\common\extmods\cmesh.cp36-win_amd64.pyd in sfepy.discrete.common.extmods.cmesh.CMesh.__reduce_cython__() TypeError: no default __reduce__ due to non-trivial __cinit__ Best regards,

4 months

Non-local boundary conditions

by michael.baumgart＠ait.ac.at

Dear SfePy Users, I want to solve a thermal problem with the following issues - several separated regions (bodies) that - exchange heat via radiation and - have anisotropic, temperature dependend material properties. The core of this problem is that the boundary conditions (heat flux given by radiation) are non-local, i.e. they depend on the dependent variable (temperature) of other boundary regions. Can I solve this kind of problem with SfePy? Thanks for input Michael Thanks Michael

5 months, 2 weeks

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